[Tutor] database question

[tpc@csua.berkeley.edu]

the easiest way to get going is to download and install MySQL and then
Python-MySQL module.  Once you have both setup a quick run of a testdb.py
script will show you how easy it is to get Python talking with MySQL:

<code>
#!/usr/bin/env python

import MySQLdb
DB = 'test'

def create_BIOINFO_table():
    conn = MySQLdb.Connection(db=DB)
    cursor = conn.cursor()
    sql = """CREATE TABLE BIOINFO (
              ACCESSION_NUMBER INT AUTO_INCREMENT PRIMARY KEY NOT NULL,
              CHROMOSOME VARCHAR(15) NOT NULL
              ) TYPE = InnoDB;"""
    result = cursor.execute(sql)
    conn.close()

create_BIOINFO_table()
</code>


On Mon, 28 Jul 2003 jpollack@socrates.Berkeley.EDU wrote:

>
> Hi,
>
> For all of you pythonistas that use the language to handle large amounts
> of data, especially in a bioinformatic context:
>
> I'm pretty new to the language and up to this point, I've been able to
> make do with storing data in a text file.  However, I'm building a tool
> that digs out data from the Genome Browser and then excises what I think
> to be putative promoter regions.  My question is this:
>
> The entirety of the file I'm generating is about 223 megabytes.  Trying to
> read in a text file of this size is just ridiculous.  I think this
> probably begs for a database application, but I"ve never used any before.
> I really don't know any SQL either, aside from the basic concept.
>
> Does anyone have any thoughts about what kind of database is python
> friendly and would be easy to use for a beginner?  Also, I assume there
> are python modules out there for populating and querying such things?
>
>
> The only fields I would have would be: Accession Number, Chromosome,
> Strand State, Hits (different database calls for the transcription start
> site... all integers), and the sequence (this is about 7000 bytes
> generally).
>
>
> Thanks so much,
>
> Joshua Pollack
>
>
>
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